Heavy metal contamination in rural soils severely threatens the food chain, and consequently, human health. The addition of organic amendments to contaminated soils is considered an effective method to immobilize heavy metals. However, the sequential decomposition of soil organic matter (SOM) still poses a risk, the re‐release of heavy metals, to animals and plants. This study aims to determine the amount of Cd and Pb in different organic fractions including dissolved organic matter, humic acid (HA), fulvic acid (FA), and residual fraction after the addition of a pine bark compost to tropical acidic soils. Four controlled samples, contaminated to 20 mg/kg, 40 mg/kg, 60 mg/kg, and 80 mg/kg for Cd, and 200 mg/kg, 400 mg/kg, 600 mg/kg, and 800 mg/kg for Pb were used in this study. The soil samples, both with and without the pine bark compost, were incubated for 120 days for further analysis. The results of the sequential extraction of organic matter indicated that the proportions of Cd and Pb were transferred from the residual fraction into the soluble HA and FA fractions after the compost was mixed into the soil. Additionally, the proportion of Cd in the soluble fraction and Pb in the HA and FA fractions elevated as incubation time increased, indicating the gradual decomposition of residual fractions and more available Cd and Pb in the soil. The diethylene triamine pentaacetic acid (DTPA) extraction result revealed an increased bioavailability of Cd and Pb after the addition of the compost that gradually increased as the organic matter in the amended soils decomposed further. Our results demonstrated that the application of pine bark compost to the soil increased the proportions of Cd in soluble fractions and Pb in humic fractions. Furthermore, we confirmed the potential risk of bioavailable Cd and Pb re‐releasing into the amended soil over time.